RBM4 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-55	BG293LV04-56
idx	0	0
TRCN#_or_BGC#	TRCN0000160719	TRCN0000160719
shRNA_or_gRNA_sequence	CCGGCCTGTTCTTCTGTCCTTCAATCTCGAGATTGAAGGACAGAAGAACAGGTTTTTTG	CCGGCCTGTTCTTCTGTCCTTCAATCTCGAGATTGAAGGACAGAAGAACAGGTTTTTTG
PAM
Name	RBM4	RBM4
Sample_ID	BG293LV04-55	BG293LV04-56
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	RBM4	RBM4
qPCR_result	87.8	83.2
Ave_qPCR	85.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9942	9943

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-55	BG293LV04-56
Sample_ID	BG293LV04-55	BG293LV04-56
Sample Name
Sample Name	RBM4-BG293LV04-55	RBM4-BG293LV04-56
RBP	RBM4	RBM4
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12534	12535

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-55	BG293LV04-56
Sample #	21	22
Sample Name	RBM4-BG293LV04-55	RBM4-BG293LV04-56
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	268	272
Peak_Molarity	68.80	61.10
libSampleQC_DNA_Well	DNA_Library_set64/set1/E11.png	DNA_Library_set64/set1/F11.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set64/set1/E7.png	RNA_Library_set64/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-55	BG293LV04-56
RBP	RBM4	RBM4
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4026	4027

Sequencing Information

	BG293LV04-55	BG293LV04-56
Sample_ID	BG293LV04-55	BG293LV04-56
Sample Name	RBM4-BG293LV04-55	RBM4-BG293LV04-56
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	21,883,820	24,711,806
total_aligned_reads	18,763,255	22,575,645
unique_aligned_reads	17,392,477	20,965,548
percent_uniqueAligned	0.79476	0.84840
correlation_replicates	0.971534	0.971534
spikein_reads	4,756	5,566
percent_spikeins	0.00022	0.00023
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2635	2636

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RBM4-BG293LV04-55_S21_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2635	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8702
RBM4-BG293LV04-55_S21_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2635	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8730
RBM4-BG293LV04-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55_S21_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV04-55_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9779
RBM4-BG293LV04-55_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55/Aligned.sortedByCoord.out.bam		ENCORE2	9807
RBM4-BG293LV04-55_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55/Aligned.sortedByCoord.out.bam		ENCORE2	9835
RBM4-BG293LV04-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55/Aligned.sortedByCoord.out.bam		ENCORE2	9863
RBM4-BG293LV04-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55/Aligned.sortedByCoord.out.bam		ENCORE2	9891
RBM4-BG293LV04-55_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2635					GRCh38	V40	RBM4-BG293LV04-55_S21_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV04-55_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9919
RBM4-BG293LV04-56_S22_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2636	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8703
RBM4-BG293LV04-56_S22_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2636	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8731
RBM4-BG293LV04-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56_S22_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV04-56_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9780
RBM4-BG293LV04-56_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56/Aligned.sortedByCoord.out.bam		ENCORE2	9808
RBM4-BG293LV04-56_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56/Aligned.sortedByCoord.out.bam		ENCORE2	9836
RBM4-BG293LV04-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56/Aligned.sortedByCoord.out.bam		ENCORE2	9864
RBM4-BG293LV04-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56/Aligned.sortedByCoord.out.bam		ENCORE2	9892
RBM4-BG293LV04-56_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2636					GRCh38	V40	RBM4-BG293LV04-56_S22_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV04-56_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9920